The Heart in the Director
by Mezzo187
Summary: Alternate ending/beginning to eps. 3.15/4.01. After being told Booth is dead, Brennan demands that Cullen let her see his body. Cullen has recognized the relationship between the two partners and helps Brennan come to terms with her reality.
1. Chapter 1

The Heart in the Director

Alternate ending/beginning to eps. 3.15/4.01. After being told Booth is dead, Brennan demands that Cullen let her see his body. Cullen recognizes the relationship between the two partners and helps Brennan come to terms with her reality.

**A/N:** _The plot bunnies are working overtime in my head, probably due to the hiatus. Even though I have two stories in-progress up here already, and several others in various stages of conception on my computer, I decided to start this one tonight. I was reading a season 3 story, which got me thinking about what happened that season, and how it ended…etc. And I always wished they would have brought Cullen back after season 1, so I decided to bring him back here as Director. This story probably won't be long, only a few chapters, so I can get back to my other stories. _;-)

* * *

Chapter 1

"I'm sorry to inform you that Agent Booth did not survive the surgery. His blood loss was too great," the surgeon said, briefly shutting his eyes. Dr. Joshua Belden wished he could close his ears, as well, as the too-familiar sounds of grief began to fill the hospital waiting room. Glancing around at all those gathered to hear the news, it was clear that this man had been well-loved. Dr. Belden understood that his job entailed telling patients' families that their loved one had passed away, but he was currently very unhappy that his job tonight included _lying_ to this patient's family and causing them what he felt was needless pain. However, he was a good citizen of the United States, and when the F.B.I. asked you to lie about the status of an active F.B.I. agent to aid in a matter of national security, he felt unable to say no. The Hippocratic oath kept him from harming patients, but he couldn't shake the feeling that he was harming these people by making them believe that Agent Booth wasn't coming back. There was one woman in particular who troubled him. She was the one still covered in his blood, the one who had ridden over in the ambulance and then been shoved away by the emergency personnel. He had overheard enough of the conversation in the waiting room to discover that she was Dr. Temperance Brennan, the agent's work partner, and that the bullet which had wounded him had actually been attended for her. She appeared almost unemotional when the doctor had delivered the news, but Dr. Belden had been watching her closely. He knew enough about people to detect the pain behind her eyes.

The surgeon was interrupted in his thoughts by the approach of the man who was the root cause of the unnecessary anguish: F.B.I. Director Sam Cullen. Dr. Belden noticed that Dr. Brennan had been watching Cullen's movements and was now advancing toward them.

"Dr. Belden, if I could speak to you in private for a moment," Cullen said, the emotion in his voice unforced since he knew how much he was hurting Booth's friends and family.

Before the men could leave the waiting room, Brennan spoke to Cullen: "Director Cullen, when you are finished with the surgeon, I would like to speak to _you_ privately as well." Cullen noticed the determined look in the scientist's eyes, one he had seen many times as she worked on finding the perpetrator in murder cases. He would need to tell her something personally—she was not the kind of woman to be satisfied with the surgeon's pronouncement.

"All right, Dr. Brennan. Take a seat, and I will be with you in a few minutes," Cullen said, his mind racing as he tried to decide how to deal with the difficult anthropologist.

* * *

"_Agent Booth did not survive the surgery."_ These were the only words that Dr. Brennan's genius mind could comprehend. _Booth is dead. Booth isn't coming back_. Her mind restated this terrible fact in multiple ways, trying to help her consciousness absorb the devastating truth. She knew there had been a chance of this—she had seen him get shot in the chest, and she had felt his blood spurting out of the wound as she tried to hold it back. The EMTs had seemed to have the bleeding under control by the time they reached the hospital, although Booth had not regained consciousness. Brennan knew that Booth was strong and had been shot before and lived, so she had not truly prepared herself for the possibility that he might not recover. When the surgeon had entered the waiting room and had not looked positive, she had tried to keep her protective walls strong. However, she had not been able to completely repel the feeling of intense pain which had assaulted her when she heard the news. She knew she would only regain her equilibrium once she had a clinical assessment of his injuries, and once she had seen his body for herself. Merely hearing about his condition without being able to see it for herself did not seem sufficiently real to the empirical scientist. She needed proof before she could completely believe in anything , even if the person telling her the information was an acknowledged expert.

When she saw Director Cullen emerge from the anxious crowd in the waiting room, she knew that he was the person who could best help her find the answers she needed. He appeared unsurprised when she approached him and requested to speak with him. He promised to talk to her after he finished talking to Booth's surgeon. Satisfied, she sat back down to wait, hoping that her emotional detachment would not fail her now when she needed it the most.

* * *

Cullen and Dr. Belden exchanged glances once they were in a hallway out of sight of those in the waiting room. Cullen spoke first.

"Doctor, it's obvious that you are uncomfortable with lying to Agent Booth's friends, but I can assure you that this is necessary," Cullen said, trying to infuse his belief in this mission into his tone of voice. He was largely successful, although the Belden could tell that Cullen wished the situation were different as well.

"It just seems so cruel, to tell them he is dead when he will make a full recovery. He clearly has many people who love him." The surgeon was visibly upset. "I tell far too many of my patients' families bad news—it seems wrong to deprive this group of their good news. They should be celebrating!"

Cullen sighed. "I know this is difficult for you. You were very convincing in there, and we at the F.B.I. appreciate that."

Belden gave Cullen a sad smile. "It was not difficult to feel badly about telling them such horrible news, especially when that news was untrue." He paused, then continued: "I will be checking back in on the patient in a few hours, when he should be fully awake. As I told you before, he should only need to stay in the hospital for another 24 hours, and then he can be transferred to wherever you need him to go." The surgeon gave Cullen another dissatisfied look then made his way deeper into the bowels of the hospital.

Watching him go, Cullen thought about what the other man had said, especially his comment about the people who loved Booth. Cullen had suspected for some time that the feelings which Agent Booth and Dr. Brennan had for each other had progressed well beyond simply being partners. It was clear that his best crime-fighting team considered each other as friends, and Cullen was beginning to believe there might even be more to their relationship than that. His first inkling of deeper feelings was instigated by Booth's actions of several occasions. First, Booth had rushed off to New Mexico because Brennan's best friend's boyfriend was missing. Granted, that had turned out to be a murder case involving counterfeiting and international criminals, but there was no way for any of them to know that ahead of time. Brennan had asked, and Booth had immediately jumped on several flights to get himself across the country overnight. Next, only a few weeks later, he had again hurried to Brennan's side when she herself was the victim of a crime while working in the Katrina aftermath of New Orleans. After his promotion to Director, Cullen had kept an eye on them largely because of their assistance in uncovering the truth about his daughter's illness. The subsequent behavior patterns of the two partners seemed to have led to this moment, when Booth had deliberately placed himself in the path of a bullet aimed at Brennan.

Once Booth was awake and fully cognizant of the new operation, he would need to prepare a list of people whom he wanted the Bureau to inform that he was not actually dead. Cullen had no doubt that Brennan would be at the top of that list, and he knew that she was probably the most trustworthy person on it. In situations like this, usually only immediate family members were informed, and it was often sometimes difficult for them to act appropriately to convince the necessary parties that the agent in question was actually missing or dead. Cullen knew that Brennan would never do anything that would jeopardize Booth's life or his cover. He decided that he might as well tell her now, and let her see Booth, rather than make her wait and find out later.

* * *

**A/N:** _To me, this just makes so much more sense than what they did on the show. Of course, I recognize that they had their reasons, but…_


	2. Chapter 2

**A/N:** _Here's the next chapter, where Brennan gets to see Booth! I didn't get as far as I wanted to—the muse has been very flighty and finicky lately. That's why I haven't been updating my other stories. But I WILL, I promise, sometime before this Thursday's episode. BTW, this chapter is a bit longer than usual._

_

* * *

_Chapter 2

Although Dr. Brennan had taken a seat in the waiting area as Cullen has requested, the director was not surprised to find her literally on the edge of her seat. As soon as she saw him re-enter the room, she rose and approached him.

"Dr. Brennan, if you would just follow me, I will answer your questions the best that I can," Cullen said, keeping his voice low, hoping no one else would insist on joining their tete-a-tete.

Brennan merely nodded and followed him back through the door and down the hall, away from her friends. Their comfort was empty now—the only person who could really comfort her in a time like this was the one person she could not have with her.

Brennan spoke first. "Director Cullen, I appreciate you taking the time to speak with me. I would appreciate, as I'm sure Dr. Saroyan would as well, a full inventory of Agent Booth's injuries. It is hard to believe someone as strong as Booth would be felled by a bullet in this way, but…" Her voice trailed off as she became lost in her own thoughts.

She seemed to rally herself back into the present and continued: "And although it is probably against protocol," Cullen felt rather than saw her stop walking as she said this, apparently to punctuate her request, "I would personally appreciate being able to see Booth's body." Cullen looked into her eyes then, and he could see the battle between grief and determination being waged there. "I am aware that this is probably an odd request, but as a scientist…"

Brennan's explanation was cut off by Cullen's voice as he interrupted her. "Dr. Brennan, I am taking you to see Agent Booth right now. Then I can give you the rest of the information you're looking for." He tried to keep his tone as neutral as possible. Cullen was personally glad that he could give at least one of Booth's friends the peace of mind of knowing his true condition.

She was clearly surprised that he had acquiesced so quickly, but then she simply nodded and followed him into the elevator. When he hit the button for the seventh floor, Brennan finally spoke again. "Isn't this hospital's morgue in the basement?" she asked.

Cullen allowed himself a small smile. "Booth isn't in the basement." He was deliberately avoiding the phrase "Booth's body" and wondered if Dr. Brennan had picked up on that yet. However, although she stared curiously at him, she seemed content to keep her turbulent thoughts to herself for now, focusing on the fact that she would finally get to see Booth and confirm what the doctor had told them.

The elevator came to a halt and a "ding" was heard, indicating that they had arrived at the requested floor. Cullen exited first, followed closely by Dr. Brennan. They walked in silence down the hallway, turning a corner before approaching a room with an armed guard waiting outside of it. As always, Brennan's mind was working and analyzing her surroundings and situation. _So Booth hasn't been transferred to the morgue yet. But why would they need to guard his body? That does not make any sense_.

The guard looked in their direction, nodding at Cullen but seeming surprised to see Brennan. After Cullen briefly nodded back at the guard, the guard resumed his stance outside the door as Cullen and Brennan entered the room.

Brennan could not keep a gasp from exiting her mouth—Booth was in the room, and he did not look dead. He was clearly injured and hooked up to various monitoring machines, but those machines were making the normal, reassuring sounds that indicated that the patient was alive and in relatively stable condition. As she drew closer to the bed, Brennan could see Booth's chest rise and fall on its own—no respiration aids were present. As she looked at his face, she saw that his color, while paler than normal, looked far better than she would have expected. His expression seemed almost calm—he was apparently only unconscious.

She turned back toward Cullen, who had remained just inside the door, with a hundred questions in her eyes. Cullen allowed himself to smile sincerely this time as he prepared himself for her verbal onslaught. However, the usually unflappable anthropologist seemed to be momentarily at a loss for words. Cullen could see the dominant emotion of sadness being replaced by a tentative expression of hope.

Brennan finally managed to say, "Booth is…alive?" The disbelief was evident in her voice, although Booth's appearance in the room confirmed that her statement was correct.

Cullen was still smiling, and finally decided that she had grasped enough of the situation for him to start his explanation. "Yes, Agent Booth was _not_ mortally wounded, although his situation was critical when he was brought to the hospital. Luckily you were there at the scene to put pressure on his wound, and the ambulance was called right away. The surgery was successful—he did not even need to be put in intensive care. You're wondering, of course, why we told all of you that he was dead."

Brennan nodded her head, keeping silent as she waited for Cullen to discuss his reasoning.

"Once the Bureau was informed that Agent Booth was shot, and how serious his condition was, we in the upper ranks remembered that there was a certain fugitive whom Booth had been chasing several years ago. This man—and don't ask me for any details, because it's classified—said that no one would ever see him again unless it was at Booth's funeral," Cullen continued.

Brennan stepped in and said, "So you decided to fake Booth's death to try and flesh out this man?"

Cullen looked confused for a moment, then realization dawned upon him. "Oh, you mean 'flush' out, Dr. Brennan, as a hunter flushes out game."

"Oh," she said. "Thank you for the clarification. At least you didn't laugh—that's what Booth usually does," she remarked, glancing over at the agent who was ostensibly sleeping peacefully.

Cullen suppressed a chuckle at this insight into the relationship between the two partners. If they could laugh at each other—and still keep working so well together—then maybe they stood a chance as a couple despite the obvious differences between the two of them.

"So, the official news is that Booth was killed in the line of duty. Because of the amount of paperwork involved in a situation like this, and to be sure our man has enough time to make it to D.C. from wherever he is now, the funeral will probably be in about two weeks. The normal protocol is for the agent in question to make a list of people to give to the Bureau to inform that he or she is not really dead. Since I am sure that you would be on Booth's list, and because of your obvious _friendship_ with him, I saw no reason to make you wait a few days until the dust settles." Cullen couldn't resist the vocal inflection of the word 'friendship,' and he was almost eager to see how Brennan responded.

If Cullen thought he could provoke Dr. Brennan into an emotional response, he was sadly mistaken. She took a few seconds to process what he said, before she replied, "I see. That sounds like a logical course of action." She paused, and Cullen thought that maybe she would say something about how pleased she was that Booth was alive. However, she merely asked, "When will he be awake? Could I sit with him until then?"

Cullen shook his head slightly. He should have known better—Dr. Brennan was famous for her lack of emotional displays. Cullen had found that he appreciated her dispassion when it came to corpses and crime scenes, although he would not have minded seeing proof of his suspicion about how she felt about her partner.

"According to the doctor, he should be awake in another hour or so, perhaps even sooner. You may stay—please have the doctor call me once Booth wakes up," Cullen said. Brennan had already turned her attention to Booth, but her eyes were drawn back to the director as he said, "And I will tell the rest of your team that I allowed you to say goodbye to Booth, and then an agent drove you home."

Brennan smiled at him. "Thank you. Booth will appreciate having a familiar face here when he regains consciousness. And do not worry—I will not tell anyone the truth about Booth's condition and will endeavor to act appropriately whenever I encounter our friends."

"I know that I can trust you, Dr. Brennan, or I would not have brought you back here," Cullen said. "I'll see you again later after Booth wakes up." Cullen quickly exited the room, thinking that Booth was lucky to have such a strong woman to care about him.

* * *

The first thing Booth was aware of was the combination of smells. He could smell antiseptic, which told him he was probably in a hospital. He could also smell something much nicer, something which always calmed him. It was the unique mixture of aromas which told him that his partner was in the room, and close to him: her perfume, her shampoo, and a few other things that he could not single out. The realization that Bones was near made him smile, even though his increasing consciousness was also making him realize he was in a fair amount of pain.

"Bones…" he said, in a voice that was half-whisper, half-groan. He hadn't used his voice in hours and his throat was dry.

Brennan immediately rose to her feet, holding a cup of water with a straw in it towards him. "Here you go, Booth, just have a little sip," she said, afraid he would drink too fast. She started to move away from the bed, but Booth reached out and grabbed her arm to stop her.

"Hey! Where are you going?" he asked, unable to keep himself from sounding like a whining little boy.

Brennan smiled. If Booth was able to whine like Parker, he must not be feeling too poorly. "I just need to let the nurse know that you're awake. Director Cullen will then be in soon to talk to you."

"OK," Booth said, but the expression on his face told her he wasn't happy about it.

Brennan smiled a little broader at Booth's pouting, then she quickly poked her head out the door. She told the guard that Booth was awake and that the doctor and Cullen should be notified. Then she returned to her chair at Booth's bedside. She gave him another drink of water, then placed the cup on the table next to his bed. She allowed herself to gaze into his rich brown eyes for a moment, just a moment, and relish the fact that he was really here, that he was still alive and looking back at her.

Booth caught her looking at him, displaying far more emotion than she usually did. He was secretly very glad that she was so happy to see him, but he was worried, too. He had been injured before, but the look he saw in her eyes was different.

"Bones, what's wrong? I know you're happy to see me, and glad that I'm awake and OK, but did something happen that I should know about?" Booth asked. Brennan looked a little startled at his intuitive inquiry, and she realized that she had allowed too much of her relief and happiness at his being alive to bleed into her face.

She tried to school her features into a more neutral appearance as she contemplated how to answer him. "You were very seriously injured Booth…" Brennan could tell by Booth's expression that that generic answer was not going to satisfy him.

Brennan sighed, and then decided that she needed to tell him the truth, even if Cullen would have preferred to inform Booth of the situation himself. It was not in Brennan's nature to be anything less than explicitly honest.

"When your surgeon came into the waiting room to update us on your condition," she began, trying not to think about how she had felt when she saw the look on the doctor's face as he approached them, "he informed us that you had not survived the surgery."

"What?" Booth exclaimed. "Everyone was told that I was dead? Why?" Booth's mind was trying to invent a logical scenario to explain this strange development, but his thoughts were almost overrun by his worry over Brennan's reaction. Just the memory of hearing the news of his death had brought a haunted look into her eyes that he had seen before—when she learned of her mother's death. He was preparing to be angry at whoever had subjected her to this, when he had a brainstorm about what was the only likely explanation.

"It was the F.B.I.'s idea…" she began, but she was quickly interrupted by Booth's next outburst.

"They're going to fake my death and use it for some kind of operation?" he broke in, clearly upset about this idea. "That's just what I need…" he muttered, almost to himself.

Brennan saw no need to explain what she knew about the plan, since she was sure Cullen would be providing Booth with all of the details once the director returned to the room. She waited to see if Booth wanted to say anything else or ask any more questions. His next question caught her off guard, however.

"Are you O.K., Bones?" he asked, realizing his memories of the incident were somewhat fuzzy. "Did you get hurt?" He forgot his own problems for a moment and focused his energy on his partner.

Brennan's reaction surprised him—she let out a somewhat choked laugh. "You've been shot in the chest, and then I had to tell you that the F.B.I. has decided to use this situation for something else potentially dangerous, and you're worried about me?" she asked incredulously.

Booth gave her a warm smile—she still didn't realize how important she was to him. "I'm always worried about you, Bones. At least, I am when I'm not right next to you keeping you safe."

Brennan smiled a little at that—she did appreciate his protectiveness even if she fought him on it. "I can take care of myself, Booth," she said, repeating the statement she had made to him many times before. He smiled back, knowing that this push-and-pull for dominance was an important part of their relationship. He also knew that he would never stop protecting her, at least as long as he had any choice in the matter.

Brennan sobered a little when the implication of his question dawned on her. "You don't really remember what happened after you were shot, do you? I would guess that is normal with this kind of traumatic injury." She was still concerned about his physical health, although mentally he seemed perfectly fine.

Neither partner had heard the door open to admit Director Cullen and Dr. Belden. The doctor started to walk towards his patient, but Cullen motioned to him to wait for a moment. Booth was clearly lucid, and Cullen wanted to hear Booth's version of the night's events.

* * *

**A/N: **_Hehehe! What will B&B say and do if they don't realize they're being watched? ;-)_


End file.
